[English] 日本語
Yorodumi
- PDB-3u6r: Three dimensional structure of broadly neutralizing anti - Hepati... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u6r
TitleThree dimensional structure of broadly neutralizing anti - Hepatitis C virus (HCV) glycoprotein E2 single chain FV fragment 1:7
Components
  • Antibody 1:7 (Heavy chain)
  • Antibody 1:7 (Light chain)
KeywordsIMMUNE SYSTEM / Ig-like domain / neutralizing single chain FV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsGilmartin, A.A. / Lamp, B. / Ruemenapf, T. / Persson, A.A. / Rey, F.A. / Krey, T.
CitationJournal: Protein Eng.Des.Sel. / Year: 2012
Title: High-level secretion of recombinant monomeric murine and human single-chain Fv antibodies from Drosophila S2 cells.
Authors: Gilmartin, A.A. / Lamp, B. / Rumenapf, T. / Persson, M.A. / Rey, F.A. / Krey, T.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Antibody 1:7 (Heavy chain)
L: Antibody 1:7 (Light chain)
A: Antibody 1:7 (Heavy chain)
B: Antibody 1:7 (Light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9945
Polymers61,8984
Non-polymers961
Water1,04558
1
H: Antibody 1:7 (Heavy chain)
L: Antibody 1:7 (Light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0453
Polymers30,9492
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-27 kcal/mol
Surface area10690 Å2
MethodPISA
2
A: Antibody 1:7 (Heavy chain)
B: Antibody 1:7 (Light chain)


Theoretical massNumber of molelcules
Total (without water)30,9492
Polymers30,9492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.485, 105.744, 105.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Antibody Antibody 1:7 (Heavy chain)


Mass: 15723.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT-scFv-Strep / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody Antibody 1:7 (Light chain)


Mass: 15225.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT-scFv-Strep / Production host: Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.54M ammonium sulfate, 0.2M lithium sulfate, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2011
RadiationMonochromator: Channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.67→37.36 Å / Num. all: 17118 / Num. obs: 15834 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 58.77 Å2
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1316 / % possible all: 54.1

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FKU

3fku


Resolution: 2.67→24.57 Å / Cor.coef. Fo:Fc: 0.9265 / Cor.coef. Fo:Fc free: 0.8905 / SU R Cruickshank DPI: 0.943 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Maximum Likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 990 6.27 %RANDOM
Rwork0.1902 ---
all0.1967 17077 --
obs0.1929 15793 92.48 %-
Displacement parametersBiso mean: 50.58 Å2
Baniso -1Baniso -2Baniso -3
1--6.4315 Å20 Å20 Å2
2---1.3103 Å20 Å2
3---7.7417 Å2
Refine analyzeLuzzati coordinate error obs: 0.315 Å
Refinement stepCycle: LAST / Resolution: 2.67→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 5 58 3667
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013698HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.195030HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1230SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes539HARMONIC5
X-RAY DIFFRACTIONt_it3698HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion20.23
X-RAY DIFFRACTIONt_chiral_improper_torsion483SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4202SEMIHARMONIC4
LS refinement shellResolution: 2.67→2.85 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2604 108 5.91 %
Rwork0.2382 1719 -
all0.2396 1827 -
obs-1827 92.48 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more